Molecular phylogenetics and evolution of turtles

Turtles are one of Earth's most instantly recognizable life forms, distinguished for over 200 million years in the fossil record. Even so, key nodes in the phylogeny of turtles remain uncertain. To address this issue, we sequenced >90% of the nuclear recombination activase gene 1 (RAG-1) for 24 species representing all modern turtle families. RAG-1 exhibited negligible saturation and base composition bias, and extensive base composition homogeneity. Most of the relationships suggested by prior phylogenetic analyses were also supported by RAG-1 and, for at least two critical nodes, with a much higher level of support. RAG-1 also indicates that the enigmatic Platysternidae and Chelydridae, often considered sister taxa based on morphological evidence, are not closely related, although their precise phylogenetic placement in the turtle tree is still unresolved. Although RAG-1 is phylogenetically informative, our research revealed fundamental conflicts among analytical methods for estimating phylogenetic hypotheses. Maximum parsimony analyses of RAG-1 alone and in combination with two mitochondrial genes suggest the earliest phylogenetic splits separating into three basal branches, the pig-nosed turtles (Carettochelyidae), the softshell turtles (Trionychidae), and a clade comprising all remaining extant turtles. Maximum likelihood and Bayesian analyses group Carettochelyidae and Trionychidae (=Trionychoidae) in their more traditional location as the sister taxon to all other hidden-necked turtles, collectively forming the Cryptodira. Our research highlights the utility of molecular data in identifying issues of character homology in morphological datasets, while shedding valuable light on the biodiversity of a globally imperiled taxon.     

Zinc proteomes, phylogenetics and evolution

Evolution has not been studied in detail with reference to the changing environment. This requires a study of the inorganic chemistry of organisms, especially metalloproteins. The evolution of organisms has been analysed many times previously using comparative studies, fossils, and molecular sequences of proteins, DNA and 16s rRNA (Zhang and Gladyshev, Chem. Rev., 2009, 109, 4828). These methods have led to the confirmation of Darwin's original proposal that evolution followed from natural selection in a changing environment often pictured as a tree. In all cases, the main tree in its upper later reaches has been well studied but its lower earlier parts are not so well defined. To approach this topic we have treated evolution as due to the intimate combination of the effect of chemical changes in the environment and in the organisms (Williams and da Silva, The Chemistry of Evolution, 2006, Elsevier). The best chemicals to examine are inorganic ions as they are common to both. As a more detailed example of the chemical study of organisms we report in this paper a bioinformatic approach to the characterization of the zinc proteomes. We deduce them from the 821 totally sequenced DNA of organisms available on NCBI, exploiting a published method developed by one of us (Andreini, Bertini and Rosato, Acc. Chem. Res., 2009, 42, 1471). Comparing the derived zinc-finger-containing proteins and zinc hydrolytic enzymes in organisms of different complexity there is a correlation in their changes during evolution related to environmental change.     

Bayesian phylogenetics using an RNA substitution model applied to early mammalian evolution

We study the phylogeny of the placental mammals using molecular data from all mitochondrial tRNAs and rRNAs of 54 species. We use probabilistic substitution models specific to evolution in base paired regions of RNA. A number of these models have been implemented in a new phylogenetic inference software package for carrying out maximum likelihood and Bayesian phylogenetic inferences. We describe our Bayesian phylogenetic method which uses a Markov chain Monte Carlo algorithm to provide samples from the posterior distribution of tree topologies. Our results show support for four primary mammalian clades, in agreement with recent studies of much larger data sets mainly comprising nuclear DNA. We discuss some issues arising when using Bayesian techniques on RNA sequence data.     

Marine turtle mitogenome phylogenetics and evolution

The sea turtles are a group of cretaceous origin containing seven recognized living species: leatherback, hawksbill, Kemp's ridley, olive ridley, loggerhead, green, and flatback. The leatherback is the single member of the Dermochelidae family, whereas all other sea turtles belong in Cheloniidae. Analyses of partial mitochondrial sequences and some nuclear markers have revealed phylogenetic inconsistencies within Cheloniidae, especially regarding the placement of the flatback. Population genetic studies based on D-Loop sequences have shown considerable structuring in species with broad geographic distributions, shedding light on complex migration patterns and possible geographic or climatic events as driving forces of sea-turtle distribution. We have sequenced complete mitogenomes for all sea-turtle species, including samples from their geographic range extremes, and performed phylogenetic analyses to assess sea-turtle evolution with a large molecular dataset. We found variation in the length of the ATP8 gene and a highly variable site in ND4 near a proton translocation channel in the resulting protein. Complete mitogenomes show strong support and resolution for phylogenetic relationships among all sea turtles, and reveal phylogeographic patterns within globally-distributed species. Although there was clear concordance between phylogenies and geographic origin of samples in most taxa, we found evidence of more recent dispersal events in the loggerhead and olive ridley turtles, suggesting more recent migrations (<1Myr) in these species. Overall, our results demonstrate the complexity of sea-turtle diversity, and indicate the need for further research in phylogeography and molecular evolution.     

Copper proteomes, phylogenetics and evolution

This paper is a continuation of our study of the connection between the changing environment and the changing use of particular elements in organisms in the course of their combined evolution (Decaria, Bertini and Williams, Metallomics, 2010, 2, 706). Here we treat the changes in copper proteins in historically the same increasingly oxidising environmental conditions. The study is a bioinformatic analysis of the types and the numbers of copper domains of proteins from 435 DNA sequences of a wide range of organisms available in NCBI, using the method developed by Andreini, Bertini and Rosato in Accounts of Chemical Research 2009, 42, 1471. The copper domains of greatest interest are found predominantly in copper chaperones, homeostatic proteins and redox enzymes mainly used outside the cytoplasm which are in themselves somewhat diverse. The multiplicity of these proteins is strongly marked. The contrasting use of the iron and heme iron proteins in oxidations, mostly in the cytoplasm, is compared with them and with activity of zinc fingers during evolution. It is shown that evolution is a coordinated development of the chemistry of elements with use of novel and multiple copies of their proteins as their availability rises in the environment.     

Ethical issues associated with HIV phylogenetics in HIV transmission dynamics research: A review of the literature using the Emanuel Framework

The reduced costs of DNA sequencing and the use of such data for HIV‐1 clinical management and phylogenetic analysis have led to a massive increase of HIV‐1 sequences in the last few years. Phylogenetic analysis has shed light on the origin, spread and characteristics of HIV‐1 epidemics and outbreaks. Phylogenetic analysis is now also being used to advance our knowledge of the drivers of HIV‐1 transmission in order to design effective interventions. However, HIV phylogenetic analysis presents unique ethical challenges, which have not been fully explored. This review presents an analysis of what appear to be key ethical issues in HIV phylogenetics in the hope of stimulating further conceptual and empirical work in this rapidly emerging area. We structure the review using the Emanuel Framework, a systematic, holistic framework, which has been adapted for use in developing countries, which bear the brunt of the HIV‐1 pandemic.     

Mitochondrial phylogenetics and evolution of mysticete whales

The phylogenetic relationships among baleen whales (Order: Cetacea) remain uncertain despite extensive research in cetacean molecular phylogenetics and a potential morphological sample size of over 2 million animals harvested. Questions remain regarding the number of species and the monophyly of genera, as well as higher order relationships. Here, we approach mysticete phylogeny with complete mitochondrial genome sequence analysis. We determined complete mtDNA sequences of 10 extant Mysticeti species, inferred their phylogenetic relationships, and estimated node divergence times. The mtDNA sequence analysis concurs with previous molecular studies in the ordering of the principal branches, with Balaenidae (right whales) as sister to all other mysticetes base, followed by Neobalaenidae (pygmy right whale), Eschrichtiidae (gray whale), and finally Balaenopteridae (rorquals + humpback whale). The mtDNA analysis further suggests that four lineages exist within the clade of Eschrichtiidae + Balaenopteridae, including a sister relationship between the humpback and fin whales, and a monophyletic group formed by the blue, sei, and Bryde's whales, each of which represents a newly recognized phylogenetic relationship in Mysticeti. We also estimated the divergence times of all extant mysticete species, accounting for evolutionary rate heterogeneity among lineages. When the mtDNA divergence estimates are compared with the mysticete fossil record, several lineages have molecular divergence estimates strikingly older than indicated by paleontological data. We suggest this discrepancy reflects both a large amount of ancestral polymorphism and long generation times of ancestral baleen whale populations.     

Molecular phylogenetics of Melastomataceae and Memecylaceae: implications for character evolution

Melastomataceae are among the most abundant and diversified groups of plants throughout the tropics, but their intrafamily relationships and morphological evolution are poorly understood. Here we report the results of parsimony and maximum likelihood (ML) analyses of cpDNA sequences from the rbcL and ndhF genes and the rpl16 intron, generated for eight outgroups (Crypteroniaceae, Alzateaceae, Rhynchocalycaceae, Oliniaceae, Penaeaceae, Myrtaceae, and Onagraceae) and 54 species of melastomes. The sample represents 42 of the family's currently recognized ～150 genera, the 13 traditional tribes, and the three subfamilies, Astronioideae, Melastomatoideae, and Memecyloideae (= Memecylaceae DC.). Parsimony and ML yield congruent topologies that place Memecylaceae as sister to Melastomataceae. Pternandra, a Southeast Asian genus of 15 species of which five were sampled, is the first- branching Melastomataceae. This placement has low bootstrap support (72%), but agrees with morphological treatments that placed Pternandra in Melastomatacaeae because of its acrodromal leaf venation, usually ranked as a tribe or subfamily. The interxylary phloem islands found in Memecylaceae and Pternandra, but not most other Melastomataceae, likely evolved in parallel because Pternandra resembles Melastomataceae in its other wood characters. A newly discovered plesiomorphic character in Pternandra, also present in Memecylaceae, is a fibrous anther endothecium. Higher Melastomataceae lack an endothecium as do the closest relatives of Melastomataceae and Memecylaceae. The next deepest split is between Astronieae, with anthers opening by slits, and all remaining Melastomataceae, which have anthers opening by pores. Within the latter, several generic groups, corresponding to traditional tribes, receive solid statistical support, but relationships among them, with one exception, are different from anything predicted on the basis of morphological data. Thus, Miconieae and Merianieae are sister groups, and both are sister to a trichotomy of Bertolonieae, Microlicieae + Melastomeae, and Dissochaeteae + Blakeeae. Sonerileae/Oxysporeae are nested within Dissochaeteae, Rhexieae within Melastomeae, and African and Asian Melastomeae within neotropical Melastomeae. These findings have profound implications for our understanding of melastome morphological evolution (and biogeography), implying, for example, that berries evolved from capsules minimally four times, stamen connectives went from dorsally enlarged to basal/ventrally enlarged, and loss of an endothecium preceded poricidal dehiscence.     

Molecular phylogenetics of Hypoxidaceae--evidence from plastid DNA data and inferences on morphology and biogeography

Phylogenetic relationships of the monocot family Hypoxidaceae (Asparagales), which occurs mainly in the Southern Hemisphere, were reconstructed using four plastid DNA regions (rbcL, trnL intron, trnL-F intergenic spacer, and trnS-G intergenic spacer) for 56 ingroup taxa including all currently accepted genera and seven species of the closely related families Asteliaceae, Blandfordiaceae, and Lanariaceae. Data were analyzed by applying parsimony, maximum likelihood and Bayesian methods. The intergenic spacer trnS-G--only rarely used in monocot research--contributed a substantial number of potentially parsimony informative characters. Hypoxidaceae consist of three well-supported major clades, but their interrelationships remain unresolved. Our data indicate that in the Pauridia clade one long-distance dispersal event occurred from southern Africa to Australia. Long-distance dispersal scenarios may also be likely for the current distribution of Hypoxis, which occurs on four continents. In the Curculigo clade, the present distribution of Curculigo s.s. on four continents could support a Gondwanan origin, but the level of divergence is too low for this hypothesis to be likely. The main clades correspond well with some floral characters, habit and palynological data, whereas chromosomal data exhibit plasticity and probably result from polyploidization and subsequent dysploidy and/or aneuploidy. Evolutionary flexibility is also suggested by the number of reported pollination syndromes: melittophily, myophily, sapromyophily, and cantharophily. Based on our phylogenetic results, we suggest cautious nomenclatural reorganization to generate monophyly at the generic level.     

PAL: an object-oriented programming library for molecular evolution and phylogenetics.

Phylogenetic Analysis Library (PAL) is a collection of Java classes for use in molecular evolution and phylogenetics. PAL provides a modular environment for the rapid construction of both special-purpose and general analysis programs. PAL version 1.1 consists of 145 public classes or interfaces in 13 packages, including classes for models of character evolution, maximum-likelihood estimation, and the coalescent, with a total of more than 27000 lines of code. The PAL project is set up as a collaborative project to facilitate contributions from other researchers. AVAILIABILTY: The program is free and is available at http://www.pal-project.org. It requires Java 1.1 or later. PAL is licensed under the GNU General Public License.     

The evolution of ecomorphological traits within the Abrothrichini (Rodentia: Sigmodontinae): a Bayesian phylogenetics approach

The generally accepted hypothesis regarding the origin of fossorial mammals proposes adaptive convergence from open environments towards the use of subterranean environments. We evaluated this hypothesis for South American mole-mice using conventional and Bayesian frameworks, with independent evidence. By using a molecular approach based on Cytochrome b and IRBP sequences, we evaluated phylogenetic relationships, time of origin, the ancestral trait of fossoriality, and ancestral distributions of species belonging to the Andean Clade (Rodentia: Sigmodontinae). Our results indicate that the Andean Clade is highly sustained; with one clade grouping all fossorial forms and another grouping all cursorial species. We hypothesized that fossoriality originated in the Miocene/Pliocene transition, in the Temperate Forests of southern South America. We conclude that the origin of fossorial ecomorphological traits did not necessarily occur under a general model of open environments, the origin of these traits depends on the ecological-historical relationship of the taxon with the environment.     

Divergent evolution within protein superfolds inferred from profile-based phylogenetics

Many dissimilar protein sequences fold into similar structures. A central and persistent challenge facing protein structural analysis is the discrimination between homology and convergence for structurally similar domains that lack significant sequence similarity. Classic examples are the OB-fold and SH3 domains, both small, modular beta-barrel protein superfolds. The similarities among these domains have variously been attributed to common descent or to convergent evolution. Using a sequence profile-based phylogenetic technique, we analyzed all structurally characterized OB-fold, SH3, and PDZ domains with less than 40% mutual sequence identity. An all-against-all, profile-versus-profile analysis of these domains revealed many previously undetectable significant interrelationships. The matrices of scores were used to infer phylogenies based on our derivation of the relationships between sequence similarity E-values and evolutionary distances. The resulting clades of domains correlate remarkably well with biological function, as opposed to structural similarity, indicating that the functionally distinct sub-families within these superfolds are homologous. This method extends phylogenetics into the challenging "twilight zone" of sequence similarity, providing the first objective resolution of deep evolutionary relationships among distant protein families.     

Molecular phylogenetics of Elateriformia (Coleoptera): evolution of bioluminescence and neoteny

Phylogenetic relationships in the coleopteran Series Elateriformia (click beetles, jewel beetles, fireflies and allies) were investigated using > 3800 nucleotides of partial nuclear (small and large subunit rRNA genes) and mitochondrial (large subunit rRNA and cytochrome oxidase subunit I) gene sequences. The Elateriformia includes several soft‐bodied lineages, some of which retain larviform features in the adult stage (neoteny), and several major bioluminescent groups, including the families Lampyridae (fireflies), Phengodidae and Rhagophthalmidae whose relationships have been contentious. All recognized superfamilies (Elateroidea, Cantharoidea, Byrrhoidea, Buprestoidea, Dascilloidea, Scirtoidea) and 28 of the 37 families, represented in 112 individuals, were included in the analysis. Sequence alignment was based on static and dynamic homology assignments and partial removal of sequences of uncertain homology. Alignment variable regions caused a great deal of uncertainty but also contributed much of the phylogenetic signal that was insufficient to resolve deep relationships when these were removed. The main features of most analyses were the monophyly of Elateroidea + Cantharoidea (= Elateroidea sensu lato), with Omethidae + Telegeusidae frequently occupying the basal node in this group; the affinities of Dascilloidea, Buprestoidea and a (broadly paraphyletic) Byrrhoidea, with unclear relationships among them; and the monophyly of Scirtoidea (including Decliniidae) as a rather distant outgroup to all others. When mapped on the resulting trees, soft‐bodied lineages were polyphyletic, contradicting the former Cantharoidea that had been united by this trait. Transitions to neoteny were either simultaneous with, or subsequent to, the origin of soft‐bodiedness in a minimum of seven lineages. The bioluminescent groups Lampyridae (including the enigmatic genus Drilaster) and the tightly allied Phengodidae + Rhagophthalmidae were never monophyletic. The former showed close relationship to the species‐rich, soft‐bodied families Lycidae and Cantharidae, while the latter grouped with poorly resolved lineages at the base of Elateridae (click beetles). Hence, although key features as soft‐bodiedness, neoteny and bioluminescence in Coleoptera are largely confined to the Elateriformia, they appear to result from multiple origins, showing the propensity of closely related lineages to acquire similar features independently. © The Willi Hennig Society 2007.     

Morphological phylogenetics of theAsteraceae-Asteroideae,with notes on character evolution

The relationships within theAsteraceae-Asteroideae are scrutinized by means of cladistic analyses of morphological and chemical data. New data are presented, and novel interpretations of features previously used in cladistic analyses are made. Examples are insertion of anther filaments in the corolla, and morphology of disc floret styles, respectively. The results include a polyphyletic or paraphyleticInuleae s. l., and a paraphyleticHeliantheae s.l. in which theEupatorieae constantly form a subclade. Comparisons are made with previous cladistic analyses of morphological data, and those acquired from molecular data. Speculations about the evolution of certain organs are presented.     

Molecular phylogenetics and evolution of maternal care in Membracine treehoppers

The treehopper subfamily Membracinae (Insecta: Hemiptera: Membracidae) comprises the majority of genera and species diversity in the New World tropics. These treehoppers exhibit a wide range of social behaviors, making them an excellent group for studying patterns of social evolution in insects. However, to date the tribal and generic relationships have remained unclear. We reconstructed the phylogeny of the Membracinae using a combined mitochondrial (COI, COII, tRNA-Leu, and 12S) and nuclear (Wg) gene data set. A total of 2608 aligned nucleotide sites were obtained for 112 species, representing 25 of 38 currently recognized genera and all four tribes. A strict consensus of five equally parsimonious trees recovered the subfamily and three of its four tribes. The majority rule consensus tree derived from the Bayesian analyses based on the GTR+I+G and mixed-models recovered many clades shared with the parsimony trees and is identical to the single best tree inferred from maximum likelihood analysis, aside from the rearrangement of one node. A comparison of mitochondrial and nuclear genes indicated that Wg provided higher consistency index (CI), data decisiveness (DD), partitioned Bremer support (PBS) than any of the mitochondrial genes analyzed. The combined mitochondrial and nuclear DNA provide strong support for the monophyly of the subfamily and three of its four tribes (Aconophorini, Hoplophorionini, and Hypsoprorini). Membracini is paraphyletic with respect to Hoplophorionini and contains two lineages, the Membracini sensu strictu and the newly resurrected tribe Bolbonotini. Our analyses show that there is a strong phylogenetic component to the evolution of maternal care. Given the widespread occurrence of maternal care within the subfamily, this trait is estimated to have < or = 3 origins, two reversals, and one loss. Our results suggest that the evolution of maternal care in insects may not be as evolutionarily labile as previously thought.     

Sequence evolution of mitochondrial tRNA genes and deep-branch animal phylogenetics

Mitochondrial DNA sequences are often used to construct molecular phylogenetic trees among closely related animals. In order to examine the usefulness of mtDNA sequences for deep-branch phylogenetics, genes in previously reported mtDNA sequences were analyzed among several animals that diverged 20–600 million years ago. Unambiguous alignment was achieved for stem-forming regions of mitochondrial tRNA genes by virtue of their conservative secondary structures. Sequences derived from stem parts of the mitochondrial tRNA genes appeared to accumulate much variation linearly for a long period of time: nearly 100 Myr for transition differences and more than 350 Myr for transversion differences. This characteristic could be attributed, in part, to the structural variability of mitochondrial tRNAs, which have fewer restrictions on their tertiary structure than do nonmitochondrial tRNAs. The tRNA sequence data served to reconstruct a well-established phylogeny of the animals with 100% bootstrap probabilities by both maximum parsimony and neighbor joining methods. By contrast, mitochondrial protein genes coding for cytochrome b and cytochrome oxidase subunit I did not reconstruct the established phylogeny or did so only weakly, although a variety of fractions of the protein gene sequences were subjected to tree-building. This discouraging phylogenetic performance of mitochondrial protein genes, especially with respect to branches originating over 300 Myr ago, was not simply due to high randomness in the data. It may have been due to the relative susceptibility of the protein genes to natural selection as compared with the stem parts of mitochondrial tRNA genes. On the basis of these results, it is proposed that mitochondrial tRNA genes may be useful in resolving deep branches in animal phylogenies with divergences that occurred some hundreds of Myr ago. For this purpose, we designed a set of primers with which mtDNA fragments encompassing clustered tRNA genes were successfully amplified from various vertebrates by the polymerase chain reaction.Abbreviations AA stem amino acid-acceptor stem - AC stem anticodon stem - COI cytochrome oxidase subunit I - cytb cytochrome b - D stem dihydrouridine stem - MP maximum parsimony - mtDNA mitochondrial DNA - Myr million years - NJ neighbor joining - PCR polymerase chain reaction - Ti transition - T stem tC stem - Tv transversion Correspondence to: Y. Kumazawa     

Genomic inferences from Afrotheria and the evolution of elephants

Recent genetic studies have established that African forest and savanna elephants are distinct species with dissociated cytonuclear genomic patterns, and have identified Asian elephants from Borneo and Sumatra as conservation priorities. Representative of Afrotheria, a superordinal clade encompassing six eutherian orders, the African savanna elephant was among the first mammals chosen for whole-genome sequencing to provide a comparative understanding of the human genome. Elephants have large and complex brains and display advanced levels of social structure, communication, learning and intelligence. The elephant genome sequence might prove useful for comparative genomic studies of these advanced traits, which have appeared independently in only three mammalian orders: primates, cetaceans and proboscideans.